Tutorials: Difference between revisions

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== Example calculations ==
== Downloads ==


=== Basic structure calculation ===
* Latest [[Media:cyana-3.98.15bin-240312Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (12.03.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).


== INCLAN Tutorials ==


  read upl demo.upl # read upper distance bounds
* [[Writing and using INCLAN macros]]
  read aco demo.aco # read dihedral angle restraints
* [[Using INCLAN variables]]
 
* [[Using INCLAN control statements]]
  calc_all 50 steps=4000 # calculate conformers
 
 
== CYANA Tutorials ==
  overview demo.ovw structures=10 pdb # analyze and write best conformers
 
* [[Defining non-standard residues]]
<!--
* [[eNORA and multi-state structure calculations]]
-->
 
== CYANA example calculations ==
 
* [[Basic structure calculation starting from given restraints]]
* [[Structure calculation using manually assigned NOESY peak lists]]
* [[Structure calculation with automated NOESY assignment]]
* [[Homodimer structure calculation with automated NOESY assignment]]
* [[ENORA and multi-state structure calculations]]
* [[Identification of key NOEs]]
* [[Determination of the protein state populations]]
* [[Determination of the protein number of states]]
* [[Peaklist preparation for eNOE pipeline]]
<!--
* [[Structure calculations using residual dipolar coupling restraints]]
* [[Structure calculations using pseudocontact shift restraints]]
* [[Various additional tasks]]
** [[Analyze a structure]]
** [[Angle restraints based on CA chemical shifts]]
** [[Create restraints for disulfide bonds]]
** [[Systematic local conformation analysis]]
** [[Create restraints for hydrogen bonds]]
** [[Merge multiple restraints files]]
** [[Migrate data from Cyana 1.x or Dyana]]
** [[Migrate data from Xplor or CNS]]
** [[Modify upper distance limits]]
** [[NOE statistics and plots]]
** [[Prepare files for PDB and BMRB deposition]]
** [[Create restraints to close flexible PRO rings]]
** [[Ramachandran plot and rotamer restraints]]
** [[Renumber chemical shifts and peaks]]
** [[Calculate RMSD values and mean structures]]
** [[Angle restraints from the program TALOS]]
-->
 
== Courses ==
 
=== Biomolecular NMR: Advanced tools PhD course ===
 
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])
 
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]
 
<!--
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===
 
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])
 
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]
 
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)-->
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)
-->
 
== Input file formats ==
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Residue library file]] (.lib)
* [[Sequence file]] (.seq)
* [[Distance restraint file]] (.upl, .lol)
* [[Torsion angle restraint file]] (.aco)
* [[Residual dipolar coupling restraint file]] (.rdc)
* [[Pseudocontact shift restraint file]] (.pcs)
* [[DG Cartesian coordinate file]] (.cor)
* [[PDB coordinate file]] (.pdb)
* [[Torsion angle file]] (.ang)
* [[XEASY chemical shift list file]] (.prot)
* [[BMRB chemical shift list file]] (.bmrb)
* [[XEASY peak list file]] (.peaks)
* [[NMRView peak list file]] (.xpk)
</div>

Revision as of 00:53, 13 March 2024

Downloads

  • Latest demo version of CYANA 3.98.15 for Linux and MacOS (12.03.2024)
    The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.
  • On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.
  • Results of all CYANA 3.98.13 demo calculations (93 MB).

INCLAN Tutorials

CYANA Tutorials

CYANA example calculations

Courses

Biomolecular NMR: Advanced tools PhD course

Gothenburg, 27 September - 8 October 2021 (course homepage)


Input file formats

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